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- EMDB-52228: Structure of the Thermus termophillus transhydrogenase -

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Basic information

Entry
Database: EMDB / ID: EMD-52228
TitleStructure of the Thermus termophillus transhydrogenase
Map dataFull cryo-EM map of the nicotinamide transhydrogenase from Thermus termophilus. The map was obtained after using the phenix-sharpened tool on the post-processing the global refinement.
Sample
  • Complex: The entitre structure of transhydrogenase from Thermus termophillus, with the NADP ligand in the DIII subunit
    • Protein or peptide: proton-translocating NAD(P)(+) transhydrogenase
    • Protein or peptide: NAD(P) transhydrogenase subunit beta
    • Protein or peptide: proton-translocating NAD(P)(+) transhydrogenase
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
KeywordsTranshydrogenase / complex / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton-translocating NAD(P)+ transhydrogenase activity / proton-translocating NAD(P)+ transhydrogenase / NADPH regeneration / NADP binding / oxidoreductase activity / plasma membrane
Similarity search - Function
NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain ...NAD(P) transhydrogenase, alpha subunit, C-terminal / 4TM region of pyridine nucleotide transhydrogenase, mitoch / NADP transhydrogenase, beta subunit / NADP transhydrogenase beta-like domain / NAD(P) transhydrogenase beta subunit / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / DHS-like NAD/FAD-binding domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
proton-translocating NAD(P)(+) transhydrogenase / proton-translocating NAD(P)(+) transhydrogenase / NAD(P) transhydrogenase subunit beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsTrasnea PI / Sazanov L
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)101020697European Union
CitationJournal: To Be Published
Title: Structure of the Thermus termophillus transhydrogenase
Authors: Trasnea PI / Sazanov L
History
DepositionDec 2, 2024-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52228.png

Downloads & links

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Map

FileDownload / File: emd_52228.map.gz / Format: CCP4 / Size: 13.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull cryo-EM map of the nicotinamide transhydrogenase from Thermus termophilus. The map was obtained after using the phenix-sharpened tool on the post-processing the global refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.84 Å/pix.
x 160 pix.
= 134.4 Å		0.84 Å/pix.
x 149 pix.
= 125.16 Å		0.84 Å/pix.
x 148 pix.
= 124.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.2
Minimum - Maximum-4.5909185 - 11.093514000000001
Average (Standard dev.)-0.000000000015253 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin11010780
Dimensions149148160
Spacing160149148
CellA: 134.4 Å / B: 125.159996 Å / C: 124.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52228_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52228_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The entitre structure of transhydrogenase from Thermus termophill...

EntireName: The entitre structure of transhydrogenase from Thermus termophillus, with the NADP ligand in the DIII subunit
Components
  • Complex: The entitre structure of transhydrogenase from Thermus termophillus, with the NADP ligand in the DIII subunit
    • Protein or peptide: proton-translocating NAD(P)(+) transhydrogenase
    • Protein or peptide: NAD(P) transhydrogenase subunit beta
    • Protein or peptide: proton-translocating NAD(P)(+) transhydrogenase
  • Ligand: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Supramolecule #1: The entitre structure of transhydrogenase from Thermus termophill...

SupramoleculeName: The entitre structure of transhydrogenase from Thermus termophillus, with the NADP ligand in the DIII subunit
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Thermus thermophilus (bacteria) / Location in cell: Membrane
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: proton-translocating NAD(P)(+) transhydrogenase

MacromoleculeName: proton-translocating NAD(P)(+) transhydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: proton-translocating NAD(P)+ transhydrogenase
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 9.909746 KDa
Recombinant expressionOrganism: Thermus thermophilus (bacteria)
SequenceString:
MEFGFWSALY IFVLTAFLGY ELITRVPVIL HTPLMSGSNF IHGVVVVGAM VVLGHAETGL EKLIGFLGVI LGAANAAGGY AVTVRMLEM FER

UniProtKB: proton-translocating NAD(P)(+) transhydrogenase

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Macromolecule #2: NAD(P) transhydrogenase subunit beta

MacromoleculeName: NAD(P) transhydrogenase subunit beta / type: protein_or_peptide / ID: 2
Details: The region from 264PHE to 273VAL was deleted from the model because of no density present in the map
Number of copies: 2 / Enantiomer: LEVO / EC number: proton-translocating NAD(P)+ transhydrogenase
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 47.371906 KDa
Recombinant expressionOrganism: Thermus thermophilus (bacteria)
SequenceString: MDLIQAAYFV VAILFIVGLK RMAHPTTAKS GIVWAGWGMV LAVLATFFWP GMGNFALILL ALLLGSVVAW WAAVRVAMTD MPQMVAIYN GMGGGAAATI AAVELLKGAF ENTGLMALAI LGGLIGSVAF TGSLIAFAKL QGIMKSRPIL FPGQKAVNAL V LALTVVIG ...String:
MDLIQAAYFV VAILFIVGLK RMAHPTTAKS GIVWAGWGMV LAVLATFFWP GMGNFALILL ALLLGSVVAW WAAVRVAMTD MPQMVAIYN GMGGGAAATI AAVELLKGAF ENTGLMALAI LGGLIGSVAF TGSLIAFAKL QGIMKSRPIL FPGQKAVNAL V LALTVVIG LSLLWNDATA SIVLFFLLAL LFGVLMTLPI GGGDMPVAIS FYNAFTGMAV GFEGFAVGNP ALMVAGTLVG AA GTLLTVL MARAMNRSVW SVLVGGFGVE QEAGEVKGSL KPIDVEDAAV MLAYAGKVVF VPGYGMALSQ AQHKLKELAD LLE ARGVEV KFAIHPVAGR MPGHMNVLLA EAGVDYDKLK DLEEINPEFP TVDVAVVIGA NDVVNPAARR PGSPLYGMPI LDVD KAKNV IVIKRGQGKG FAGVENELFY AENTRMLYGD AQKVLTELIQ ALKRL

UniProtKB: NAD(P) transhydrogenase subunit beta

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Macromolecule #3: proton-translocating NAD(P)(+) transhydrogenase

MacromoleculeName: proton-translocating NAD(P)(+) transhydrogenase / type: protein_or_peptide / ID: 3
Details: The region from SER219 to LEU230 and ALA 256 to ARG262 was deleted from the model because of no density present in the map
Number of copies: 2 / Enantiomer: LEVO / EC number: proton-translocating NAD(P)+ transhydrogenase
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightTheoretical: 39.894332 KDa
Recombinant expressionOrganism: Thermus thermophilus (bacteria)
SequenceString: MVTVAVPKER APGERRVALV PEVVARLVKG GARVRVERGA GEGAYHPDEA YQEAGAEVVE RGELLKGAHL LFTVQPPPED LIQALEPGA IVVGFVQPHK NLELVRALQA KKATVIAMEL IPRITRAQSM DALSSQATVA GYLAAIHAAR LSPRFFPMLT T AAGTIRPA ...String:
MVTVAVPKER APGERRVALV PEVVARLVKG GARVRVERGA GEGAYHPDEA YQEAGAEVVE RGELLKGAHL LFTVQPPPED LIQALEPGA IVVGFVQPHK NLELVRALQA KKATVIAMEL IPRITRAQSM DALSSQATVA GYLAAIHAAR LSPRFFPMLT T AAGTIRPA KVMVMGVGVA GLMAIATAKR LGAQVFAYDV RKAALEQALS LGAKPIELPI SAEGEGGYAR ELTEEEKRIQ HE ALRDHVA GMDVLITTAQ VPGRRAPILL TEDMVERLKP GTVVVDLAAE SGGNCVLTKP GEVVEVRGVR VYGPLNLPSE LSV HASEMY AKNLYNLSSL LIEKGAFAPK WEDEIVRAAL LMKEGEVLHG PTKALLG

UniProtKB: proton-translocating NAD(P)(+) transhydrogenase

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Macromolecule #4: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: NAP
Molecular weightTheoretical: 743.405 Da
Chemical component information

ChemComp-NAP:
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMHEPESHEPES
0.02 %DDMN-Dodecyl-beta-D-maltoside
0.1 %CHAPSCHAPS

Details: 150mM NaCl, 50mM HEPES, 0.02% DDM and CHAPS was added right before vitrification
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.092 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: Vitrification carried out.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4772 / Average exposure time: 2.4 sec. / Average electron dose: 89.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4o9u

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114749
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4o9u


Chain - Source name: Other / Chain - Initial model type: other / Details: 4O9U
Output model

PDB-9hjx:
Structure of the Thermus termophillus transhydrogenase

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